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{{f5samples
{{f5samples
|id=FF:11256-116F5
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000065,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001004,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0005423
|name=Small Airway Epithelial Cells, donor1
|sample_id=11256
|rna_tube_id=116F5
|rna_box=116
|rna_position=F5
|sample_cell_lot=lot:4F0715
|sample_cell_catalog=CC-2547
|sample_company=Lonza
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=19 years old adult
|sample_tissue=lung
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=19
|sample_ethnicity=C
|rna_rin=10
|rna_od260/230=2.11
|rna_od260/280=2.026666667
|sample_cell_type=pneumocyte
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=35.45666667
|rna_concentration=1.611666667
|sample_note=
|profile_hcage=CNhs10884,LSID703,release008,COMPLETED
|profile_cagescan=NCig10047,,,
|profile_srnaseq=SRhi10007,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000548,CL:0002076,CL:0002321,CL:0002368,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000548,CL:0002076,CL:0002321,CL:0002368,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000065,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001004,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0005423
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=TBX4,5:2.57567062192;TP53:2.26545298905;ZEB1:2.02721516287;TEF:1.98432170019;PPARG:1.94285274747;HIF1A:1.69518714745;SNAI1..3:1.60160122063;VSX1,2:1.27717533249;MYOD1:1.24804721494;NKX2-2,8:1.19346155503;ONECUT1,2:1.17518335877;HOX{A4,D4}:0.968922153354;ADNP_IRX_SIX_ZHX:0.96275527045;TEAD1:0.95378758598;NKX3-2:0.924467226586;TFCP2:0.89681759554;HAND1,2:0.851417772994;UFEwm:0.838301735272;PAX4:0.826130776781;PAX1,9:0.820681185295;T:0.815486075552;ARID5B:0.77263668612;FOXQ1:0.742454837232;ELK1,4_GABP{A,B1}:0.728844461636;NKX2-1,4:0.705151552246;HSF1,2:0.701476262146;TLX2:0.657444671195;NKX2-3_NKX2-5:0.638713638237;HLF:0.622978564914;SPZ1:0.611429482649;CRX:0.601345761447;ZNF148:0.59086170358;LMO2:0.582496962764;CEBPA,B_DDIT3:0.578137852563;IKZF1:0.56823058149;FOS_FOS{B,L1}_JUN{B,D}:0.499788444643;TBP:0.492646439258;GLI1..3:0.460888474948;FOSL2:0.457452061061;XCPE1{core}:0.44913690296;SOX17:0.448119848038;SP1:0.421165267517;bHLH_family:0.420767608522;FOXM1:0.420263187189;BACH2:0.339361994371;MTF1:0.337381863538;KLF4:0.33077484453;FOXN1:0.319190283862;FOXL1:0.316710875494;ESR1:0.297470012536;EVI1:0.253446805782;LHX3,4:0.222480992585;STAT5{A,B}:0.206599816926;PDX1:0.172652138112;PAX5:0.168855834747;TFAP2{A,C}:0.160721942302;NR6A1:0.152521611356;NKX3-1:0.147464921591;CDC5L:0.144805549179;NR5A1,2:0.140293529235;HMX1:0.139126820326;HMGA1,2:0.129158869537;NFIL3:0.12472042446;ZBTB6:0.122562197236;MAFB:0.0821821668727;PAX2:0.0806434747503;EP300:0.0759453788246;ZNF238:0.0588294499704;NFE2:0.0460920448165;RBPJ:0.0404975253404;EBF1:0.0371564349485;ATF4:0.0310203567542;MAZ:0.0297483950387;ALX4:0.0176842116075;PAX6:0.0156406053124;ELF1,2,4:0.0113508979592;POU6F1:0.00603596207525;REST:-0.00201286053028;AR:-0.0155689504753;FOXO1,3,4:-0.0204642334099;MYBL2:-0.0382584870213;ZIC1..3:-0.0509616891608;NFIX:-0.053935020148;NR1H4:-0.0546335215609;SMAD1..7,9:-0.0572210444739;TFAP4:-0.0629215665427;ZNF143:-0.0837384145903;NHLH1,2:-0.0881795502337;HNF1A:-0.105394221152;PAX8:-0.105972211353;NFKB1_REL_RELA:-0.108347422848;FOX{F1,F2,J1}:-0.115604303192;TLX1..3_NFIC{dimer}:-0.120228651563;ZBTB16:-0.128418903927;GZF1:-0.137516990536;AIRE:-0.139390980682;ZNF423:-0.140880000598;EN1,2:-0.158320681435;IRF7:-0.165564467154;POU3F1..4:-0.169405721617;GFI1B:-0.195522881323;NRF1:-0.205547469845;POU2F1..3:-0.209262857761;RXR{A,B,G}:-0.209955784575;STAT2,4,6:-0.218557898888;YY1:-0.242082785142;SOX2:-0.262878616002;HOX{A5,B5}:-0.2768712306;NANOG:-0.279297889597;STAT1,3:-0.279455739901;LEF1_TCF7_TCF7L1,2:-0.292510259779;GTF2A1,2:-0.297694385146;ATF6:-0.303774400354;FOX{I1,J2}:-0.306810135868;MED-1{core}:-0.319089767493;HOX{A6,A7,B6,B7}:-0.321857421414;RXRA_VDR{dimer}:-0.329047361535;ETS1,2:-0.337707140282;FOXP3:-0.337797557874;POU1F1:-0.341044076889;ATF5_CREB3:-0.348117905497;HIC1:-0.364657964291;SPI1:-0.365632303175;HNF4A_NR2F1,2:-0.368604999058;TOPORS:-0.378389273268;TFAP2B:-0.381812952233;HES1:-0.390395903919;GTF2I:-0.394281573078;OCT4_SOX2{dimer}:-0.408553282611;GATA6:-0.411899733946;NR3C1:-0.417390259456;NKX6-1,2:-0.419543457987;MYB:-0.42805229423;NFE2L2:-0.438475085852;MYFfamily:-0.459695886429;NFE2L1:-0.461753181336;AHR_ARNT_ARNT2:-0.463229770238;JUN:-0.481084330334;CDX1,2,4:-0.491677244109;RREB1:-0.497013386796;ZFP161:-0.500545655491;SPIB:-0.507228317312;MTE{core}:-0.523469362342;ZNF384:-0.528750222377;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.536863013253;CREB1:-0.543865496871;RFX1:-0.549620930579;ALX1:-0.594162741592;GCM1,2:-0.61427588819;PRDM1:-0.615849799574;RORA:-0.627013327378;RFX2..5_RFXANK_RFXAP:-0.627822313274;RUNX1..3:-0.628144752719;FOXA2:-0.628622129184;EGR1..3:-0.632138847641;ATF2:-0.642002502124;PITX1..3:-0.653200182958;ESRRA:-0.658971229405;POU5F1:-0.68240169846;NANOG{mouse}:-0.695276280385;PRRX1,2:-0.714833850847;DBP:-0.718166154093;SRF:-0.722862627536;HOXA9_MEIS1:-0.727158340648;MEF2{A,B,C,D}:-0.746389728806;FOX{D1,D2}:-0.784316542616;PBX1:-0.791372419047;PATZ1:-0.794489354376;TFDP1:-0.79820749074;BPTF:-0.827898904999;GFI1:-0.845638809371;CUX2:-0.852460279804;IRF1,2:-0.898252152296;E2F1..5:-0.923450633802;NFATC1..3:-0.923720824314;NFY{A,B,C}:-0.929248862475;FOXP1:-0.935611456099;DMAP1_NCOR{1,2}_SMARC:-0.962434802066;SREBF1,2:-0.974142691251;HBP1_HMGB_SSRP1_UBTF:-0.980501850108;IKZF2:-0.981986446008;MZF1:-1.02055847125;SOX{8,9,10}:-1.02270900006;TGIF1:-1.02736806599;TAL1_TCF{3,4,12}:-1.05712725252;GATA4:-1.11050415725;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.1186697119;XBP1:-1.16512637296;BREu{core}:-1.23928871479;FOXD3:-1.33312042038;PAX3,7:-1.45023696828;SOX5:-1.4980414842
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11256-116F5
|is_a=EFO:0002091;;FF:0000002;;FF:0000166;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000166;;FF:0000210
|name=Small Airway Epithelial Cells, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10047,,,
|profile_hcage=CNhs10884,LSID703,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10007,,,
|rna_box=116
|rna_catalog_number=N/A
|rna_concentration=1.611666667
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.11
|rna_od260/280=2.026666667
|rna_position=F5
|rna_rin=10
|rna_sample_type=total RNA
|rna_tube_id=116F5
|rna_weight_ug=35.45666667
|sample_age=19
|sample_cell_catalog=CC-2547
|sample_cell_line=
|sample_cell_lot=lot:4F0715
|sample_cell_type=pneumocyte
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Lonza
|sample_description=
|sample_dev_stage=19 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=11256
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=lung
|top_motifs=TBX4,5:2.57567062192;TP53:2.26545298905;ZEB1:2.02721516287;TEF:1.98432170019;PPARG:1.94285274747;HIF1A:1.69518714745;SNAI1..3:1.60160122063;VSX1,2:1.27717533249;MYOD1:1.24804721494;NKX2-2,8:1.19346155503;ONECUT1,2:1.17518335877;HOX{A4,D4}:0.968922153354;ADNP_IRX_SIX_ZHX:0.96275527045;TEAD1:0.95378758598;NKX3-2:0.924467226586;TFCP2:0.89681759554;HAND1,2:0.851417772994;UFEwm:0.838301735272;PAX4:0.826130776781;PAX1,9:0.820681185295;T:0.815486075552;ARID5B:0.77263668612;FOXQ1:0.742454837232;ELK1,4_GABP{A,B1}:0.728844461636;NKX2-1,4:0.705151552246;HSF1,2:0.701476262146;TLX2:0.657444671195;NKX2-3_NKX2-5:0.638713638237;HLF:0.622978564914;SPZ1:0.611429482649;CRX:0.601345761447;ZNF148:0.59086170358;LMO2:0.582496962764;CEBPA,B_DDIT3:0.578137852563;IKZF1:0.56823058149;FOS_FOS{B,L1}_JUN{B,D}:0.499788444643;TBP:0.492646439258;GLI1..3:0.460888474948;FOSL2:0.457452061061;XCPE1{core}:0.44913690296;SOX17:0.448119848038;SP1:0.421165267517;bHLH_family:0.420767608522;FOXM1:0.420263187189;BACH2:0.339361994371;MTF1:0.337381863538;KLF4:0.33077484453;FOXN1:0.319190283862;FOXL1:0.316710875494;ESR1:0.297470012536;EVI1:0.253446805782;LHX3,4:0.222480992585;STAT5{A,B}:0.206599816926;PDX1:0.172652138112;PAX5:0.168855834747;TFAP2{A,C}:0.160721942302;NR6A1:0.152521611356;NKX3-1:0.147464921591;CDC5L:0.144805549179;NR5A1,2:0.140293529235;HMX1:0.139126820326;HMGA1,2:0.129158869537;NFIL3:0.12472042446;ZBTB6:0.122562197236;MAFB:0.0821821668727;PAX2:0.0806434747503;EP300:0.0759453788246;ZNF238:0.0588294499704;NFE2:0.0460920448165;RBPJ:0.0404975253404;EBF1:0.0371564349485;ATF4:0.0310203567542;MAZ:0.0297483950387;ALX4:0.0176842116075;PAX6:0.0156406053124;ELF1,2,4:0.0113508979592;POU6F1:0.00603596207525;REST:-0.00201286053028;AR:-0.0155689504753;FOXO1,3,4:-0.0204642334099;MYBL2:-0.0382584870213;ZIC1..3:-0.0509616891608;NFIX:-0.053935020148;NR1H4:-0.0546335215609;SMAD1..7,9:-0.0572210444739;TFAP4:-0.0629215665427;ZNF143:-0.0837384145903;NHLH1,2:-0.0881795502337;HNF1A:-0.105394221152;PAX8:-0.105972211353;NFKB1_REL_RELA:-0.108347422848;FOX{F1,F2,J1}:-0.115604303192;TLX1..3_NFIC{dimer}:-0.120228651563;ZBTB16:-0.128418903927;GZF1:-0.137516990536;AIRE:-0.139390980682;ZNF423:-0.140880000598;EN1,2:-0.158320681435;IRF7:-0.165564467154;POU3F1..4:-0.169405721617;GFI1B:-0.195522881323;NRF1:-0.205547469845;POU2F1..3:-0.209262857761;RXR{A,B,G}:-0.209955784575;STAT2,4,6:-0.218557898888;YY1:-0.242082785142;SOX2:-0.262878616002;HOX{A5,B5}:-0.2768712306;NANOG:-0.279297889597;STAT1,3:-0.279455739901;LEF1_TCF7_TCF7L1,2:-0.292510259779;GTF2A1,2:-0.297694385146;ATF6:-0.303774400354;FOX{I1,J2}:-0.306810135868;MED-1{core}:-0.319089767493;HOX{A6,A7,B6,B7}:-0.321857421414;RXRA_VDR{dimer}:-0.329047361535;ETS1,2:-0.337707140282;FOXP3:-0.337797557874;POU1F1:-0.341044076889;ATF5_CREB3:-0.348117905497;HIC1:-0.364657964291;SPI1:-0.365632303175;HNF4A_NR2F1,2:-0.368604999058;TOPORS:-0.378389273268;TFAP2B:-0.381812952233;HES1:-0.390395903919;GTF2I:-0.394281573078;OCT4_SOX2{dimer}:-0.408553282611;GATA6:-0.411899733946;NR3C1:-0.417390259456;NKX6-1,2:-0.419543457987;MYB:-0.42805229423;NFE2L2:-0.438475085852;MYFfamily:-0.459695886429;NFE2L1:-0.461753181336;AHR_ARNT_ARNT2:-0.463229770238;JUN:-0.481084330334;CDX1,2,4:-0.491677244109;RREB1:-0.497013386796;ZFP161:-0.500545655491;SPIB:-0.507228317312;MTE{core}:-0.523469362342;ZNF384:-0.528750222377;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.536863013253;CREB1:-0.543865496871;RFX1:-0.549620930579;ALX1:-0.594162741592;GCM1,2:-0.61427588819;PRDM1:-0.615849799574;RORA:-0.627013327378;RFX2..5_RFXANK_RFXAP:-0.627822313274;RUNX1..3:-0.628144752719;FOXA2:-0.628622129184;EGR1..3:-0.632138847641;ATF2:-0.642002502124;PITX1..3:-0.653200182958;ESRRA:-0.658971229405;POU5F1:-0.68240169846;NANOG{mouse}:-0.695276280385;PRRX1,2:-0.714833850847;DBP:-0.718166154093;SRF:-0.722862627536;HOXA9_MEIS1:-0.727158340648;MEF2{A,B,C,D}:-0.746389728806;FOX{D1,D2}:-0.784316542616;PBX1:-0.791372419047;PATZ1:-0.794489354376;TFDP1:-0.79820749074;BPTF:-0.827898904999;GFI1:-0.845638809371;CUX2:-0.852460279804;IRF1,2:-0.898252152296;E2F1..5:-0.923450633802;NFATC1..3:-0.923720824314;NFY{A,B,C}:-0.929248862475;FOXP1:-0.935611456099;DMAP1_NCOR{1,2}_SMARC:-0.962434802066;SREBF1,2:-0.974142691251;HBP1_HMGB_SSRP1_UBTF:-0.980501850108;IKZF2:-0.981986446008;MZF1:-1.02055847125;SOX{8,9,10}:-1.02270900006;TGIF1:-1.02736806599;TAL1_TCF{3,4,12}:-1.05712725252;GATA4:-1.11050415725;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.1186697119;XBP1:-1.16512637296;BREu{core}:-1.23928871479;FOXD3:-1.33312042038;PAX3,7:-1.45023696828;SOX5:-1.4980414842
}}
}}

Revision as of 14:50, 21 March 2012


Name:Small Airway Epithelial Cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stage19 years old adult
sexfemale
age19
cell typepneumocyte
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
CollapseHg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
CollapseHg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10884



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10884



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10884


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002321 (embryonic cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000065 (respiratory tract)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001004 (respiratory system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA